Introduction: Higher prevalence and incidence of cardiovascular disease (CVD) has been reported in the Middle-East compared to other regions. Subclinical hypothyroidism and hyperthyroidism have been shown to be related with increased risk for CVD. We aimed to investigate the relation of subclinical thyroid dysfunction with the incidence of CVD among an Iranian population. Materials and Methods: After excluding patients with overt hypothyroidism and hyperthyroidism, a total of 3822 participants entered the study (44.1% men). According to their thyrotropin and free thyroxin levels, they were categorized into 3 groups: Euthyroid, subclinical hypothyroidism and subclinical hyperthyroidism. Multivariable Cox proportional hazard models were used to assess the relation of subclinical thyroid dysfunctions with incident CVD. Results: Mean age (SD) of the participants was 46.4 (12.0) years. At baseline, no significant difference was observed in the frequency of prevalent CVD cases (n=197) between all groups. Since there was no significant interaction between prevalent CVD and thyroid function states with outcomes, participants with prevalent CVD were not excluded. A total of 387 CVD events occurred during a median follow-up of 11.2 years. Even in the age and sex adjusted model, no association was observed between different subclinical thyroid dysfunctions and incidence of CVD. The multivariable hazard ratios (95% CI) of subclinical hypothyroidism and subclinical hyperthyroidism for CVD events as compared with euthyroid state were 1.32 (0.85–2.07) and 0.89 (0.51–1.55), respectively. Conclusion: Both at baseline and in follow-up, no relation was observed between different subclinical thyroid dysfunctions and the prevalence and incidence of CVD.